Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter

Abstract

The Gram-negative Acinetobacter genus has several species of clear medical relevance. Many fully sequenced genomes belonging to the genus have been published in recent years; however, there has not been a recent attempt to infer the evolutionary history of Acinetobacter with that vast amount of information. Here, through a phylogenomic approach, we established the most up-to-date view of the evolutionary relationships within this genus and highlighted several cases of poor classification, especially for the very closely related species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex (Acb complex). Furthermore, we determined appropriate phylogenetic markers for this genus and showed that concatenation of the top 13 gives a very decent reflection of the evolutionary relationships for the genus Acinetobacter. The intersection between our top markers and previously defined universal markers is very small. In general, our study shows that, although there seems to be hardly any universal markers, bespoke phylogenomic approaches can be used to infer the phylogeny of different bacterial genera. We expect that ad hoc phylogenomic approaches will be the standard in the years to come and will provide enough information to resolve intricate evolutionary relationships like those observed in the Acb complex.

Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil

“…of Acinetobacter baumannii, and strain JUb89 is not part of the Acb complex. The findings with strains EGD AQ BF14 and NCTC7364 are consistent with a previous phylogenetic analysis of Acinetobacter that included fewer strains of A. calcoaceticus [35]. Of interest, in this previous analysis, strain ANC 3811 (which groups with A. oleivorans in our tree) formed a basal clade within A. calcoaceticus in a tree based on 225 single gene families but was grouped with A. oleivorans in a tree based on 13 top marker genes [35].…”

“…The findings with strains EGD AQ BF14 and NCTC7364 are consistent with a previous phylogenetic analysis of Acinetobacter that included fewer strains of A. calcoaceticus [35]. Of interest, in this previous analysis, strain ANC 3811 (which groups with A. oleivorans in our tree) formed a basal clade within A. calcoaceticus in a tree based on 225 single gene families but was grouped with A. oleivorans in a tree based on 13 top marker genes [35]. Our tree otherwise agreed with the evolutionary relationships presented in the 225 single gene family tree for the included A. calcoaceticus strains, but our study agreed instead with the 13 top marker gene tree in terms of the relationships between A. baumannii, A. nosocomialis, and A. seifertii.…”

“…A. calcoaceticus is known to be part of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex (Acb complex), which also includes A. baumannii, Acinetobacter lactucae, Acinetobacter nosocomialis, Acinetobacter oleivorans, Acinetobacter pittii, and Acinetobacter seifertii [35]. Species within the Acb complex can not always be differentiated by phenotypic methods [36,37], and type strains from each of these Acb complex species were included in our tree.…”

“…The tree was visualized using PhyD3 [64] and adapted in PowerPoint (Microsoft Corporation, Redmont, WA, USA). The tree was rooted with Acinetobacter brisouii, which is known to be outside of the Acb complex, and forms part of a basal cade in the Acinetobacter phylogeny [35].…”

BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters

“…Before performing any taxonomy-related diversity analysis, we ensured that all included genomes were correctly assigned to their respective taxa. Several studies pointed out that there might be a potentially widespread misclassification of bacterial genomes within the NCBI database [72][73][74]. To avoid this issue, we chose to use the taxonomy derived from the GTDB (Genome Taxonomy Database), which were posited to be more phylogenomically accurate than that of NCBI [75].…”